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- PDB-3bvv: Golgi mannosidase II D204A catalytic nucleophile mutant complex w... -

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Basic information

Entry
Database: PDB / ID: 3bvv
TitleGolgi mannosidase II D204A catalytic nucleophile mutant complex with METHYL ALPHA-D-MANNOPYRANOSYL-(1->3)-[6-THIO-ALPHA-D-MANNOPYRANOSYL-(1->6)]-BETA-D-MANNOPYRANOSIDE
ComponentsAlpha-mannosidase 2
KeywordsHYDROLASE / FAMILY 38 GLYCOYSL HYDROLASE / Glycosidase / Golgi apparatus / Membrane / Signal-anchor / Transmembrane
Function / homology
Function and homology information


mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / N-glycan processing / mannose metabolic process / Golgi stack ...mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase / mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity / rhodopsin biosynthetic process / encapsulation of foreign target / Reactions specific to the complex N-glycan synthesis pathway / mannosidase activity / alpha-mannosidase activity / N-glycan processing / mannose metabolic process / Golgi stack / : / carbohydrate binding / Golgi membrane / endoplasmic reticulum / metal ion binding
Similarity search - Function
Alpha-mannosidase 2, C-terminal sub-domain / Glycosyl hydrolases family 38 C-terminal sub-domain / Immunoglobulin-like - #1360 / : / Lysosomal alpha-mannosidase-like, central domain / Glycoside hydrolase family 38, central domain / : / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Golgi alpha-mannosidase II; domain 4 ...Alpha-mannosidase 2, C-terminal sub-domain / Glycosyl hydrolases family 38 C-terminal sub-domain / Immunoglobulin-like - #1360 / : / Lysosomal alpha-mannosidase-like, central domain / Glycoside hydrolase family 38, central domain / : / Glycoside hydrolase 38, N terminal domain / 7-stranded beta/alpha barrel / Golgi alpha-mannosidase II; domain 4 / Glycoside hydrolase family 38, N-terminal domain / Glycosyl hydrolase family 38, C-terminal / Glycoside hydrolase family 38, central domain / Glycoside hydrolase family 38, central domain superfamily / Glycosyl hydrolases family 38 N-terminal domain / Glycosyl hydrolases family 38 C-terminal domain / Alpha mannosidase middle domain / Alpha mannosidase, middle domain / Glycoside hydrolase families 57/38, central domain superfamily / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Distorted Sandwich / Alpha-Beta Barrel / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Alpha-mannosidase 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKuntz, D.A. / Rose, D.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Probing the substrate specificity of Golgi alpha-mannosidase II by use of synthetic oligosaccharides and a catalytic nucleophile mutant.
Authors: Zhong, W. / Kuntz, D.A. / Ember, B. / Singh, H. / Moremen, K.W. / Rose, D.R. / Boons, G.J.
History
DepositionJan 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Aug 5, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / pdbx_branch_scheme / pdbx_distant_solvent_atoms / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_branch_scheme.mon_id / _pdbx_branch_scheme.pdb_mon_id / _pdbx_entity_branch_link.comp_id_1 / _pdbx_entity_branch_list.comp_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id
Revision 3.1Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 3.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 3.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-mannosidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7077
Polymers119,6581
Non-polymers1,0496
Water29,8511657
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.104, 109.815, 139.303
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Alpha-mannosidase 2 / Alpha-mannosidase II / Mannosyl-oligosaccharide 1 / 3-1 / 6-alpha-mannosidase / MAN II / Golgi ...Alpha-mannosidase II / Mannosyl-oligosaccharide 1 / 3-1 / 6-alpha-mannosidase / MAN II / Golgi alpha-mannosidase II / AMAN II


Mass: 119657.602 Da / Num. of mol.: 1 / Fragment: Catalytic domain; UNP residues 76-1108 / Mutation: D204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: alpha-Man-II, GmII / Plasmid: pMTBIP_NHIS / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 cells
References: UniProt: Q24451, mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[6-thio-alpha-D-mannopyranose-(1-6)]methyl beta-D-mannopyranoside


Type: oligosaccharide / Mass: 534.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a1122h-1b_1-5_1*OC][a1122h-1a_1-5][a1122h-1a_1-5_6*S]/1-2-3/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp6SH]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 1662 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1657 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsE970K CONFLICT IN UNP ENTRY Q24451

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: TRIS, NACL, PEG6000, MPD. Crystals washed in phosphate buffered reservoir solution before soaking with substrate for 24 hrs, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 260486 / Num. obs: 254755 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.8 / % possible all: 78.4

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HTY

1hty


Resolution: 1.3→19.61 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.292 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.046 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.173 3796 1.5 %RANDOM
Rwork0.152 ---
obs0.153 254592 97.79 %-
all-260346 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.368 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.135 Å
Refinement stepCycle: LAST / Resolution: 1.3→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8581 0 49 1706 10336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0218945
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.94612233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20151123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98823.614440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.439151526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6911563
X-RAY DIFFRACTIONr_chiral_restr0.0990.21304
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026973
X-RAY DIFFRACTIONr_nbd_refined0.2040.24283
X-RAY DIFFRACTIONr_nbtor_refined0.3090.26089
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.21300
X-RAY DIFFRACTIONr_metal_ion_refined0.0070.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.288
X-RAY DIFFRACTIONr_mcbond_it1.2571.55475
X-RAY DIFFRACTIONr_mcangle_it1.79928702
X-RAY DIFFRACTIONr_scbond_it2.4333950
X-RAY DIFFRACTIONr_scangle_it3.454.53501
X-RAY DIFFRACTIONr_rigid_bond_restr1.44739425
X-RAY DIFFRACTIONr_sphericity_free4.00531693
X-RAY DIFFRACTIONr_sphericity_bonded3.40138653
LS refinement shellResolution: 1.3→1.332 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 258 -
Rwork0.187 16240 -
all-16498 -
obs--86.75 %

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